The option is run interactively: in response to prompts, the user enters the names of the two files to be merged, and the name for the merged output file. File names must be complete (i.e. the .gen suffix needs to be included). The program compares family IDs and locus names in the two input files, and for families having the same ID compares individual ID #s; it then merges the data from the two files into a single .gen file, taking overlaps into account.
A family appearing in both files need not have exactly the same individuals (in which case the output file will have a merged family with all individuals appearing in either input file); the program checks individuals which do occur in both input files to make sure their mother and father ID #s and sex agree, and if they don't displays an error message. If the two files have some loci in common, the genotypes at those loci in the output file for an individual appearing in both input files will be those from the second file.
N.B. Be careful when merging files containing, say, CEPH and disease families that there are no spurious matches between family IDs. For this purpose it is useful to use the fact that family IDs may be arbitrary character strings; so for example CEPH family IDs may be prefixed with "CEPH".
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